python313Packages.segyio: fix build
This commit is contained in:
Sigmanificient
@@ -1,47 +0,0 @@
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From 64f06c0643f1f8691a8f2757496b60f1ab98c866 Mon Sep 17 00:00:00 2001
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From: =?UTF-8?q?Sa=C3=AFd=20Benaissa?= <sbenaissa@shearwatergeo.com>
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Date: Fri, 8 Dec 2023 21:51:32 +0100
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Subject: [PATCH] Add include for cstdint, fix segyio build on fedora
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---
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lib/experimental/segyio/segyio.hpp | 1 +
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python/segyio/segyio.cpp | 1 +
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python/setup.py | 2 +-
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3 files changed, 3 insertions(+), 1 deletion(-)
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diff --git a/lib/experimental/segyio/segyio.hpp b/lib/experimental/segyio/segyio.hpp
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index 706f07ff5..7ba3ffb99 100644
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--- a/lib/experimental/segyio/segyio.hpp
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+++ b/lib/experimental/segyio/segyio.hpp
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@@ -13,6 +13,7 @@
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#include <vector>
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#include <segyio/segy.h>
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+#include <cstdint>
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/*
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* KNOWN ISSUES AND TODOs:
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diff --git a/python/segyio/segyio.cpp b/python/segyio/segyio.cpp
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index 76da965c3..bd8a8622e 100644
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--- a/python/segyio/segyio.cpp
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+++ b/python/segyio/segyio.cpp
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@@ -16,6 +16,7 @@
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#include <cstring>
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#include <sstream>
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#include <stdexcept>
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+#include <cstdint>
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#if PY_MAJOR_VERSION >= 3
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#define IS_PY3K
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diff --git a/python/setup.py b/python/setup.py
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index 6c6553bc7..654075be9 100644
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--- a/python/setup.py
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+++ b/python/setup.py
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@@ -1,6 +1,6 @@
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import os
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import sys
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-import skbuild
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+import skbuild # pip install scikit-build
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import setuptools
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long_description = """
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@@ -2,6 +2,7 @@
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lib,
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buildPythonPackage,
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fetchFromGitHub,
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fetchpatch,
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cmake,
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ninja,
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scikit-build,
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@@ -15,12 +16,11 @@ buildPythonPackage rec {
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pyproject = false; # Built with cmake
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patches = [
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# https://github.com/equinor/segyio/pull/570
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./add_missing_cstdint.patch
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# https://github.com/equinor/segyio/pull/576/
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./fix-setuptools.patch
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./explicitly-cast.patch
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./numpy-2.patch
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# Bump minimum CMake version to 3.11
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(fetchpatch {
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url = "https://github.com/equinor/segyio/commit/3e2cbe6ca6d4bc7d4f4d95666f5d2983836e8461.patch?full_index=1";
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hash = "sha256-sOBHi8meMSkxEZy0AXwebAnIVPatpwQHd+4Co5zIhLQ=";
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})
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];
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postPatch = ''
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@@ -1,32 +0,0 @@
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From eafe8476566e1d8e8b9a486ca808685cb439a767 Mon Sep 17 00:00:00 2001
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From: Sveinung Rundhovde <ssru@equinor.com>
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Date: Mon, 29 Jul 2024 10:46:35 +0200
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Subject: [PATCH] Explicitly cast from BinField to int
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Parsing segyio.BinField type as int in PyArg_ParseTuple is no longer
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possible.
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---
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python/segyio/open.py | 6 +++---
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1 file changed, 3 insertions(+), 3 deletions(-)
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diff --git a/python/segyio/open.py b/python/segyio/open.py
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index cd902c15..80bc3a5b 100644
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--- a/python/segyio/open.py
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+++ b/python/segyio/open.py
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@@ -166,8 +166,8 @@ def open(filename, mode="r", iline = 189,
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f = segyio.SegyFile(fd,
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filename = str(filename),
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mode = mode,
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- iline = iline,
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- xline = xline,
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+ iline = int(iline),
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+ xline = int(xline),
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endian = endian,
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)
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@@ -189,4 +189,4 @@ def open(filename, mode="r", iline = 189,
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if ignore_geometry:
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return f
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- return infer_geometry(f, metrics, iline, xline, strict)
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+ return infer_geometry(f, metrics, int(iline), int(xline), strict)
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@@ -1,32 +0,0 @@
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From 6df089258c2ef4356427263f652cff0c053c6173 Mon Sep 17 00:00:00 2001
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From: Sveinung Rundhovde <ssru@equinor.com>
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Date: Fri, 26 Jul 2024 15:03:33 +0200
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Subject: [PATCH] Fix attribute error in setup.py
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This line was causing a error due to an update to scikit-build. The
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issue was that the setuptools.command.test module is not put into the
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symbol table by the setuptools import, but it was put there during the
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skbuild import causing it to be available. Due to changes in
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scikit-build this is no longer the case and the line gives an
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AttributError.
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The rationale for this line was that scikit-builds test command implied
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develop (this was obnoxious), something that is no longer true. There is
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thus no longer any reason to keep this line, so we can fix this issue by
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simply removing it.
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---
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python/setup.py | 1 -
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1 file changed, 1 deletion(-)
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diff --git a/python/setup.py b/python/setup.py
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index 6c6553bc..6bae62f0 100644
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--- a/python/setup.py
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+++ b/python/setup.py
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@@ -95,7 +95,6 @@ def src(x):
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# supported OS X release 10.9
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'-DCMAKE_OSX_DEPLOYMENT_TARGET=10.9',
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],
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- cmdclass = { 'test': setuptools.command.test.test },
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classifiers = [
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'Development Status :: 5 - Production/Stable',
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'Environment :: Other Environment',
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@@ -1,34 +0,0 @@
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From 75b2156a6414e2464eb15663004b8ab928374135 Mon Sep 17 00:00:00 2001
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From: Sveinung Rundhovde <ssru@equinor.com>
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Date: Tue, 30 Jul 2024 08:32:56 +0200
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Subject: [PATCH] Fix test failing due to Numpy 2.0 promotion rules
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From Numpy 2.0 adding a numpy.float32 and a Python numeric type returns
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a numy.float32 when it previously returned a numpy.float64. This changes
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the behavior when using the Python builtin sum function on a
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numpy.float32 array as the internal computations now will be performed
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as numpy.float32 additions when it used to be numpy.float64.
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Passing a numpy.double(0) as a start value to the innermost sum forces
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the old behavior and provides consistent results for Numpy 1 and 2.
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---
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python/test/segyio_c.py | 4 ++--
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1 file changed, 2 insertions(+), 2 deletions(-)
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diff --git a/python/test/segyio_c.py b/python/test/segyio_c.py
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index 45fe95d89..b1e144d9d 100644
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--- a/python/test/segyio_c.py
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+++ b/python/test/segyio_c.py
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@@ -540,10 +540,10 @@ def read_line(f, metrics, iline_idx, xline_idx):
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buf = numpy.zeros((len(iline_idx), samples), dtype=numpy.single)
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f.getline(xline_trace0, len(iline_idx), xline_stride, offsets, buf)
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- assert sum(sum(buf)) == approx(800.061169624, abs=1e-6)
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+ assert sum(sum(buf), numpy.double(0)) == approx(800.061169624, abs=1e-6)
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f.getline(iline_trace0, len(xline_idx), iline_stride, offsets, buf)
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- assert sum(sum(buf)) == approx(305.061146736, abs=1e-6)
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+ assert sum(sum(buf), numpy.double(0)) == approx(305.061146736, abs=1e-6)
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f.close()
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